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[jalview.git] / src / jalview / appletgui / RotatableCanvas.java

diff --git a/src/jalview/appletgui/RotatableCanvas.java b/src/jalview/appletgui/RotatableCanvas.java
index 370de5f..f411a63 100755 (executable)
--- a/src/jalview/appletgui/RotatableCanvas.java
+++ b/src/jalview/appletgui/RotatableCanvas.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -99,7 +99,7 @@ public class RotatableCanvas
   {\r
     this.points = points;\r
     this.npoint = npoint;\r
-    PaintRefresher.Register(this, av.alignment);\r
+    PaintRefresher.Register(this, av.getSequenceSetId());\r
 \r
     prefsize = getPreferredSize();\r
     orig = new float[npoint][3];\r
@@ -371,18 +371,18 @@ public class RotatableCanvas
       int y = (int) ( (float) (sp.coord[1] - centre[1]) * scale) + halfheight;\r
       float z = sp.coord[1] - centre[2];\r
 \r
-      if (sp.sequence.getColor() == Color.black)\r
+      if (av.getSequenceColour(sp.sequence) == Color.black)\r
       {\r
         g.setColor(Color.white);\r
       }\r
       else\r
       {\r
-        g.setColor(sp.sequence.getColor());\r
+        g.setColor(av.getSequenceColour(sp.sequence));\r
       }\r
 \r
       if (av.getSelectionGroup() != null)\r
       {\r
-        if (av.getSelectionGroup().sequences.contains( ( (SequencePoint) points.\r
+        if (av.getSelectionGroup().getSequences(false).contains( ( (SequencePoint) points.\r
             elementAt(i)).sequence))\r
         {\r
           g.setColor(Color.gray);\r
@@ -498,7 +498,7 @@ public class RotatableCanvas
       {\r
         av.getSelectionGroup().addOrRemove(found, true);\r
         av.getSelectionGroup().setEndRes(av.alignment.getWidth()-1);\r
-        PaintRefresher.Refresh(this, av.alignment);\r
+        PaintRefresher.Refresh(this, av.getSequenceSetId());\r
       }\r
       else\r
       {\r
@@ -577,7 +577,7 @@ public class RotatableCanvas
       {\r
         if (av != null)\r
         {\r
-          if (!av.getSelectionGroup().sequences.contains(sp.sequence))\r
+          if (!av.getSelectionGroup().getSequences(false).contains(sp.sequence))\r
           {\r
             av.getSelectionGroup().addSequence(sp.sequence, true);\r
           }\r